FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 1NNZZ

Calculation Name: 2ISB-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2ISB

Chain ID: A

ChEMBL ID:
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UniProt ID: O29167

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1995532.507365
FMO2-HF: Nuclear repulsion 1922354.220378
FMO2-HF: Total energy -73178.286987
FMO2-MP2: Total energy -73386.557939


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:-3:HIS)


Summations of interaction energy for fragment #1(A:-3:HIS)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-16.406-14.7990.002-0.571-1.0370.001
Interaction energy analysis for fragmet #1(A:-3:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.970 / q_NPA : 0.967
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A-1HIS00.0350.0343.5540.2401.8470.002-0.571-1.0370.001
4A0HIS00.0550.0205.7680.9580.9580.0000.0000.0000.000
5A1MET0-0.047-0.0307.9411.2951.2950.0000.0000.0000.000
6A2VAL0-0.005-0.00111.7330.2830.2830.0000.0000.0000.000
7A3MET0-0.0350.00613.971-0.619-0.6190.0000.0000.0000.000
8A4GLU-1-0.882-0.95016.665-12.631-12.6310.0000.0000.0000.000
9A5TYR0-0.051-0.03416.660-0.458-0.4580.0000.0000.0000.000
10A6GLU-1-0.817-0.89422.252-10.456-10.4560.0000.0000.0000.000
11A7LEU0-0.037-0.01824.028-0.088-0.0880.0000.0000.0000.000
12A8ARG10.9630.97827.01010.75810.7580.0000.0000.0000.000
13A9THR0-0.0310.00030.078-0.162-0.1620.0000.0000.0000.000
14A10PRO00.037-0.00132.8910.0970.0970.0000.0000.0000.000
15A11LEU0-0.057-0.01628.818-0.280-0.2800.0000.0000.0000.000
16A12VAL00.0210.01526.0810.1450.1450.0000.0000.0000.000
17A13LYS11.0161.00526.57410.62910.6290.0000.0000.0000.000
18A14ASP-1-0.872-0.94522.326-13.259-13.2590.0000.0000.0000.000
19A15GLN0-0.125-0.07221.928-0.712-0.7120.0000.0000.0000.000
20A16ILE00.0190.01722.413-0.473-0.4730.0000.0000.0000.000
21A17LEU0-0.028-0.01521.777-0.329-0.3290.0000.0000.0000.000
22A18LYS10.9110.98317.00715.15115.1510.0000.0000.0000.000
23A19LEU0-0.062-0.00917.807-0.839-0.8390.0000.0000.0000.000
24A20LYS10.8870.94412.89119.68519.6850.0000.0000.0000.000
25A21VAL00.019-0.00117.7270.4460.4460.0000.0000.0000.000
26A22GLY0-0.039-0.02517.198-0.852-0.8520.0000.0000.0000.000
27A23ASP-1-0.817-0.90716.635-18.092-18.0920.0000.0000.0000.000
28A24VAL00.0190.00619.1220.8390.8390.0000.0000.0000.000
29A25VAL0-0.019-0.00922.127-0.328-0.3280.0000.0000.0000.000
30A26TYR0-0.025-0.01124.9120.5460.5460.0000.0000.0000.000
31A27ILE0-0.010-0.00427.699-0.259-0.2590.0000.0000.0000.000
32A28THR0-0.057-0.05630.4240.2610.2610.0000.0000.0000.000
33A29GLY00.0460.03832.384-0.217-0.2170.0000.0000.0000.000
34A30GLU-1-0.926-0.95435.284-7.698-7.6980.0000.0000.0000.000
35A31ILE0-0.047-0.02534.757-0.283-0.2830.0000.0000.0000.000
36A32PHE00.0040.00537.5830.2410.2410.0000.0000.0000.000
37A33THR0-0.0060.00639.221-0.172-0.1720.0000.0000.0000.000
38A34ALA00.0430.01240.7640.1550.1550.0000.0000.0000.000
39A35ARG10.8660.92640.8166.7666.7660.0000.0000.0000.000
40A36ASP-1-0.725-0.83642.805-7.106-7.1060.0000.0000.0000.000
41A37GLU-1-0.883-0.93545.056-6.168-6.1680.0000.0000.0000.000
42A38ALA0-0.0030.00244.9750.0430.0430.0000.0000.0000.000
43A39HIS0-0.087-0.06340.035-0.204-0.2040.0000.0000.0000.000
44A40ALA00.0120.00844.424-0.009-0.0090.0000.0000.0000.000
45A41ARG10.9170.96347.5356.0806.0800.0000.0000.0000.000
46A42ALA0-0.035-0.02444.8570.0360.0360.0000.0000.0000.000
47A43LEU0-0.036-0.02543.027-0.030-0.0300.0000.0000.0000.000
48A44GLU-1-0.902-0.93046.813-5.898-5.8980.0000.0000.0000.000
49A45TRP00.028-0.01349.3950.0660.0660.0000.0000.0000.000
50A46MET0-0.088-0.05142.265-0.045-0.0450.0000.0000.0000.000
51A47GLU-1-1.001-0.98648.002-6.325-6.3250.0000.0000.0000.000
52A48GLU-1-0.954-0.97749.987-5.749-5.7490.0000.0000.0000.000
53A49GLY0-0.060-0.01650.6360.0830.0830.0000.0000.0000.000
54A50LYS10.8880.94851.6735.8825.8820.0000.0000.0000.000
55A51GLU-1-0.944-0.97348.029-6.717-6.7170.0000.0000.0000.000
56A52LEU0-0.040-0.02144.4020.0840.0840.0000.0000.0000.000
57A53PRO0-0.025-0.00447.846-0.030-0.0300.0000.0000.0000.000
58A54PHE00.0240.00742.510-0.042-0.0420.0000.0000.0000.000
59A55SER00.0200.00640.2250.0360.0360.0000.0000.0000.000
60A56PHE00.0470.00437.905-0.134-0.1340.0000.0000.0000.000
61A57ASP-1-0.871-0.94135.727-9.134-9.1340.0000.0000.0000.000
62A58LYS10.8570.91733.2189.4089.4080.0000.0000.0000.000
63A59GLY00.0550.04434.057-0.084-0.0840.0000.0000.0000.000
64A60VAL0-0.004-0.01731.754-0.272-0.2720.0000.0000.0000.000
65A61VAL00.0100.02534.5230.2350.2350.0000.0000.0000.000
66A62TYR0-0.052-0.06435.101-0.317-0.3170.0000.0000.0000.000
67A63HIS00.1020.04535.2950.1960.1960.0000.0000.0000.000
68A64CYS0-0.048-0.02238.041-0.046-0.0460.0000.0000.0000.000
69A65GLY00.0130.01440.4920.0990.0990.0000.0000.0000.000
70A66PRO0-0.045-0.00843.4140.0100.0100.0000.0000.0000.000
71A67LEU0-0.0070.00744.6850.1620.1620.0000.0000.0000.000
72A68VAL00.006-0.00946.837-0.124-0.1240.0000.0000.0000.000
73A69LYS10.9340.97449.0896.4576.4570.0000.0000.0000.000
74A70LYS10.9570.98151.5985.7125.7120.0000.0000.0000.000
75A71ASN0-0.067-0.02853.344-0.002-0.0020.0000.0000.0000.000
76A72ASP-1-0.805-0.88953.222-6.006-6.0060.0000.0000.0000.000
77A73GLU-1-0.881-0.94248.463-6.584-6.5840.0000.0000.0000.000
78A74TRP00.014-0.01149.5090.0610.0610.0000.0000.0000.000
79A75ARG10.8590.90947.5316.3466.3460.0000.0000.0000.000
80A76VAL00.0560.02642.9590.1030.1030.0000.0000.0000.000
81A77VAL0-0.066-0.02345.047-0.056-0.0560.0000.0000.0000.000
82A78SER0-0.029-0.03542.844-0.156-0.1560.0000.0000.0000.000
83A79ALA00.0510.01939.7230.1190.1190.0000.0000.0000.000
84A80GLY00.0330.04238.186-0.252-0.2520.0000.0000.0000.000
85A81PRO00.0280.03134.8280.1470.1470.0000.0000.0000.000
86A82THR0-0.038-0.03237.4390.2330.2330.0000.0000.0000.000
87A83THR0-0.027-0.03736.779-0.221-0.2210.0000.0000.0000.000
88A84SER00.0490.01934.1630.1110.1110.0000.0000.0000.000
89A85ALA00.0250.02335.9430.0800.0800.0000.0000.0000.000
90A86ARG10.7670.85537.0377.3427.3420.0000.0000.0000.000
91A87MET00.0370.03338.1920.2180.2180.0000.0000.0000.000
92A88ASN0-0.005-0.00335.384-0.270-0.2700.0000.0000.0000.000
93A89PRO00.004-0.00137.919-0.090-0.0900.0000.0000.0000.000
94A90PHE00.0470.02840.6940.0310.0310.0000.0000.0000.000
95A91THR0-0.017-0.02234.865-0.033-0.0330.0000.0000.0000.000
96A92PRO00.0430.02035.858-0.146-0.1460.0000.0000.0000.000
97A93LYS10.9600.99737.0337.2047.2040.0000.0000.0000.000
98A94ILE0-0.019-0.00337.6800.0120.0120.0000.0000.0000.000
99A95LEU0-0.012-0.02632.357-0.072-0.0720.0000.0000.0000.000
100A96GLU-1-0.909-0.94635.634-7.905-7.9050.0000.0000.0000.000
101A97LYS10.9430.97337.3657.8057.8050.0000.0000.0000.000
102A98VAL0-0.094-0.02433.8060.0220.0220.0000.0000.0000.000
103A99GLU-1-0.873-0.92631.521-10.184-10.1840.0000.0000.0000.000
104A100CYS0-0.060-0.04429.673-0.460-0.4600.0000.0000.0000.000
105A101MET0-0.0010.01430.8400.4180.4180.0000.0000.0000.000
106A102GLY00.0230.01430.075-0.460-0.4600.0000.0000.0000.000
107A103ILE0-0.0070.00430.4530.3820.3820.0000.0000.0000.000
108A104ILE00.0190.01830.654-0.343-0.3430.0000.0000.0000.000
109A105GLY00.0250.00231.8210.3980.3980.0000.0000.0000.000
110A106LYS10.9060.96932.1047.8547.8540.0000.0000.0000.000
111A107GLY0-0.005-0.01431.6240.2460.2460.0000.0000.0000.000
112A108GLY00.0330.02830.293-0.059-0.0590.0000.0000.0000.000
113A109MET0-0.060-0.02430.5230.2700.2700.0000.0000.0000.000
114A110SER0-0.0030.00130.988-0.298-0.2980.0000.0000.0000.000
115A111GLU-1-0.735-0.86928.108-10.885-10.8850.0000.0000.0000.000
116A112GLU-1-0.940-0.95530.998-8.341-8.3410.0000.0000.0000.000
117A113VAL00.019-0.00531.138-0.061-0.0610.0000.0000.0000.000
118A114VAL0-0.018-0.01526.181-0.254-0.2540.0000.0000.0000.000
119A115GLU-1-0.895-0.94628.148-10.948-10.9480.0000.0000.0000.000
120A116ALA0-0.0010.00929.831-0.102-0.1020.0000.0000.0000.000
121A117MET0-0.038-0.01627.923-0.061-0.0610.0000.0000.0000.000
122A118ARG10.8680.95123.38911.42711.4270.0000.0000.0000.000
123A119GLY0-0.031-0.02425.5960.2960.2960.0000.0000.0000.000
124A120LYS10.8120.89326.7459.5059.5050.0000.0000.0000.000
125A121ALA0-0.0050.00727.8130.1690.1690.0000.0000.0000.000
126A122ALA00.0340.01924.963-0.427-0.4270.0000.0000.0000.000
127A123TYR0-0.005-0.02426.4390.4510.4510.0000.0000.0000.000
128A124PHE00.026-0.00725.167-0.518-0.5180.0000.0000.0000.000
129A125ALA00.001-0.00126.8580.4860.4860.0000.0000.0000.000
130A126PHE00.0400.00228.133-0.266-0.2660.0000.0000.0000.000
131A127THR0-0.046-0.03426.9570.0020.0020.0000.0000.0000.000
132A128GLY00.0480.03229.913-0.120-0.1200.0000.0000.0000.000
133A129GLY0-0.021-0.00632.3730.2610.2610.0000.0000.0000.000
134A130ALA0-0.010-0.03035.0340.0150.0150.0000.0000.0000.000
135A131GLY00.0520.01938.0070.1440.1440.0000.0000.0000.000
136A132ALA00.0020.01539.2490.0410.0410.0000.0000.0000.000
137A133LEU00.038-0.00237.8300.0270.0270.0000.0000.0000.000
138A134ALA00.0240.02336.064-0.052-0.0520.0000.0000.0000.000
139A135ALA00.0250.01637.199-0.091-0.0910.0000.0000.0000.000
140A136MET0-0.030-0.00639.2470.1660.1660.0000.0000.0000.000
141A137SER0-0.031-0.01635.399-0.068-0.0680.0000.0000.0000.000
142A138ILE0-0.034-0.01337.387-0.109-0.1090.0000.0000.0000.000
143A139LYS10.8590.95237.8168.3928.3920.0000.0000.0000.000
144A140LYS10.9080.96141.5767.0177.0170.0000.0000.0000.000
145A141VAL0-0.023-0.00143.239-0.151-0.1510.0000.0000.0000.000
146A142LYN00.0120.00543.0810.2120.2120.0000.0000.0000.000
147A143GLY00.006-0.00346.0740.1680.1680.0000.0000.0000.000
148A144VAL0-0.037-0.01047.223-0.151-0.1510.0000.0000.0000.000
149A145VAL00.0080.01247.7610.1350.1350.0000.0000.0000.000
150A146TRP00.007-0.01047.135-0.092-0.0920.0000.0000.0000.000
151A147GLU-1-0.871-0.95651.746-5.946-5.9460.0000.0000.0000.000
152A148ASP-1-0.890-0.93153.246-5.818-5.8180.0000.0000.0000.000
153A149LEU00.0060.00849.5630.0570.0570.0000.0000.0000.000
154A150GLY00.0200.02352.452-0.007-0.0070.0000.0000.0000.000
155A151MET0-0.017-0.00849.580-0.127-0.1270.0000.0000.0000.000
156A152PRO0-0.044-0.02547.245-0.123-0.1230.0000.0000.0000.000
157A153GLU-1-0.794-0.92646.156-6.907-6.9070.0000.0000.0000.000
158A154ALA0-0.0290.02347.582-0.050-0.0500.0000.0000.0000.000
159A155VAL0-0.019-0.00743.851-0.169-0.1690.0000.0000.0000.000
160A156TRP0-0.015-0.03144.2770.1150.1150.0000.0000.0000.000
161A157LEU00.0150.00942.826-0.226-0.2260.0000.0000.0000.000
162A158LEU0-0.044-0.03540.1130.1530.1530.0000.0000.0000.000
163A159GLU-1-0.864-0.93137.967-8.491-8.4910.0000.0000.0000.000
164A160VAL0-0.050-0.03334.6400.0970.0970.0000.0000.0000.000
165A161GLU-1-0.879-0.95634.146-8.705-8.7050.0000.0000.0000.000
166A162ARG10.8470.91725.99111.33511.3350.0000.0000.0000.000
167A163PHE00.0310.01831.4960.0470.0470.0000.0000.0000.000
168A164GLY0-0.0200.00429.979-0.345-0.3450.0000.0000.0000.000
169A165PRO0-0.016-0.01026.6780.3010.3010.0000.0000.0000.000
170A166CYS0-0.007-0.01326.9950.5390.5390.0000.0000.0000.000
171A167ILE00.0030.02121.813-0.473-0.4730.0000.0000.0000.000
172A168VAL0-0.015-0.00621.1780.5840.5840.0000.0000.0000.000
173A169ALA00.0250.00321.961-0.481-0.4810.0000.0000.0000.000
174A170ILE0-0.038-0.01624.1220.0640.0640.0000.0000.0000.000
175A171ASP-1-0.770-0.86519.588-14.427-14.4270.0000.0000.0000.000
176A172ALA00.0470.03222.6850.4350.4350.0000.0000.0000.000
177A173HIS0-0.064-0.05520.0210.2630.2630.0000.0000.0000.000
178A174GLY00.0070.01721.612-0.181-0.1810.0000.0000.0000.000
179A175ASN0-0.080-0.04618.4480.2990.2990.0000.0000.0000.000
180A176SER00.0620.01321.8590.2420.2420.0000.0000.0000.000
181A177LEU0-0.026-0.01920.169-0.110-0.1100.0000.0000.0000.000
182A178TYR0-0.014-0.00123.3420.0970.0970.0000.0000.0000.000
183A179ARG10.7650.87923.00112.14812.1480.0000.0000.0000.000
184A180ARG10.9690.98924.72710.93910.9390.0000.0000.0000.000